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Table 1 Comparison of exonic SNPs and indels from current analysis with known variants from different databases

From: Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication

SNPEff terms by type

Total

Common SNPs with dbSNP

Common SNPs with ensembl

Common SNPs with broad

Common variants with Orlando et al.[[8]]

Common variants with Doan et al.[[11]]

Novel variants

SNPs

       

Exon

8056

679

678

693

4650

1974

2920

Non-synonymous coding

43043

3014

3002

3026

25200

12759

15007

Non-synonymous start

10

1

1

1

3

3

5

Start lost

48

4

4

4

30

19

15

Stop gained

383

16

16

16

185

81

182

Stop lost

29

6

6

6

20

5

8

Synonymous coding

52965

4367

4355

4368

34360

16144

15962

Synonymous start

1

0

0

0

0

0

1

Synonymous stop

27

0

0

0

15

11

7

Indels

       

Codon change plus codon deletion

133

-

-

-

31

0

102

Codon change plus codon insertion

248

-

-

-

62

0

186

Codon deletion

201

-

-

-

55

1

145

Codon insertion

178

-

-

-

39

2

137

Exon

828

-

-

-

284

26

518

Exon deleted

4

-

-

-

0

0

4

Frameshift

7360

-

-

-

1903

541

4916

Start lost

7

-

-

-

2

0

5

Stop gained

25

-

-

-

6

0

19

  1. The total number of SNPs and indels per SNPEff term detected in five horses and their concordance with dbSNP, Broad Institute and Ensembl data as well as data published by Orlando et al.[8] and Doan et al.[11] are shown.